doi: 10.1038/s42003-020-01162-2.
Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations
Takashi Gakuhari # 1 2 3, Shigeki Nakagome # 4, Simon Rasmussen 5, Morten E Allentoft 5 6, Takehiro Sato 7, Thorfinn Korneliussen 5, Blánaid Ní Chuinneagáin 4, Hiromi Matsumae 3, Kae Koganebuchi 3, Ryan Schmidt 3, Souichiro Mizushima 8, Osamu Kondo 9, Nobuo Shigehara 10, Minoru Yoneda 11, Ryosuke Kimura 12, Hajime Ishida 12, Tadayuki Masuyama 13, Yasuhiro Yamada 14, Atsushi Tajima 7, Hiroki Shibata 15, Atsushi Toyoda 16, Toshiyuki Tsurumoto 17, Tetsuaki Wakebe 17, Hiromi Shitara 18, Tsunehiko Hanihara 3, Eske Willerslev 5 19 20, Martin Sikora 21, Hiroki Oota 22 23
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- PMID:32843717
- PMCID: PMC7447786
- DOI: 10.1038/s42003-020-01162-2
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Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations
Takashi Gakuhari et al. Commun Biol..
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Abstract
Anatomically modern humans reached East Asia more than 40,000 years ago. However, key questions still remain unanswered with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of the region may elucidate a more detailed picture of the peopling of East Eurasia. Here, we analyze the whole-genome sequence of a 2,500-year-old individual (IK002) from the main-island of Japan that is characterized with a typical Jomon culture. The phylogenetic analyses support multiple waves of migration, with IK002 forming a basal lineage to the East and Northeast Asian genomes examined, likely representing some of the earliest-wave migrants who went north from Southeast Asia to East Asia. Furthermore, IK002 shows strong genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration. This study highlights the power of ancient genomics to provide new insights into the complex history of human migration into East Eurasia.
Conflict of interest statement
The authors declare no competing interests.
Figures
a Principal component analysis (PCA) of ancient and present-day individuals from worldwide populations after the out-of-Africa expansion. Gray labels represent population codes showing coordinates for individuals. Colored circles indicate ancient individuals.b ADMIXTURE ancestry components (K = 15) for ancient and selected contemporary individuals. The color of light blue represents the component of IK002, which is shared with the present-day Japanese and Ulchi.c Maximum-likelihood phylogenetic tree (TreeMix) with bootstrap support of 100% unless indicated otherwise. The tree shows phylogenetic relationship among present-day Southeast/East Asians, Northeast Siberians, Native Americans, and ancient East Eurasians. Mbuti are the present-day Africans; Ust’Ishim is an Upper-Paleolithic individual (45 kya) from Western Siberia; Mal′ta (MA-1) and Sunghir is Upper-Paleolithic individuals (24 kya and 34 kya), and Loschbour is a Mesolithic individual from West Eurasia; La368 is a pre-Neolithic Hòabìnhian hunter-gatherer (8.0 kya) in Laos and Önge is the present-day hunter-gatherers in the Andaman island, both of who are from Southeast Asia; Tiányuán is an Upper-Paleolithic individual (40 kya) in Beijing, China; Kusunda are the present-day minority people in Nepal; Chokhopani is an Iron-age individual (3.0–2.4 kya) and Sherpa are the present-day minority people, both of who are in Tibet; Han, Ami and main-island Japanese are the present-day East Asians; Devils Gate Cave is a Neolithic individual (8.0 kya) in the Primorye region of Northeast Siberia, and Shamanka and Lokomotive are Early-Neolithic individuals (8.0 kya) from Central Siberia, respectively; USR1 and Clovis are late-Paleolithic individuals (11.5 kya and 12.6 kya) in Alaska and Montana, respectively,. Colored arrows represent the migration pathways and signals of admixture among all datasets. The migration weight represents the fraction of ancestry derived from the migration edge.
Three differentD values are plotted with different colors;D(Mbuti, MA-1;X, Ami) in red,D(Mbuti,X; MA-1, Ami) in cyan, andD(Mbuti, Ami;X, MA-1) in green. Error bars show three standard deviation, and the vertical dotted and dashed lines indicateD = 0 andD = −0.2, −0.1, 0.1, and 0.2.
Heatmaps off4(Mbuti, IK002;X, Chokhopani), whereX are the present-day East Eurasian populations. The color and size represents the value off4-statistics. The shape represents statistical significances of genetic affinities based onZ-score. Triangle label means statistical significance with |Z| > 3 (P < 0.01), inverted triangle means weak significance with |Z| = 2–3 and circle means non-significance with |Z| < 2 (P > 0.05).
The basal East Eurasians (bEE) are an ancient population that had no divergence among the ancestors of East Asians, Northeast Asians/East Siberian, and Native Americans. NA-ES-NA presents another ancient population that had no split between the ancestors of Northeast Asians/East Siberian and Native Americans.
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